# List of top-scoring protein chains for t2k-100-30-bys hidden Markov model. # HMM and HMM E-value scores computed by SAM (c) 1992-2001 Regents of the University of California, Santa Cruz # Sequence Alignment and Modeling Software System # http://www.cse.ucsc.edu/research/compbio/sam.html # ----------------- Citations (SAM, SAM-T99, HMMs) -------------------- # R. Hughey, A. Krogh, Hidden Markov models for sequence analysis: # Extension and analysis of the basic method, CABIOS 12:95-107, 1996. # K. Karplus, C. Barrett, R. Hughey, Hidden Markov models for detecting # remote protein homologies, Bioinformatics 14(10):846-856, 1998. # A. Krogh et al., Hidden Markov models in computational biology: # Applications to protein modeling, JMB 235:1501-1531, Feb 1994. # # FSSP representative for each protein chain taken from FSSP: # ------------------Citations (FSSP) ----------------------------------- # L. Holm and C. Sander (1996) Mapping the protein universe. Science 273:595-602. # #SCOP domains found in each protein chain taken from SCOP: # ------------------Citations (SCOP) ----------------------------------- #Murzin A. G., Brenner S. E., Hubbard T., Chothia C. (1995). #SCOP: a structural classification of proteins database for the investigation of sequences and structures. #J. Mol. Biol. 247, 536-540. Sequence_ID Length Target_Evalue FSSP-rep SCOP_domain SCOP_suid 5S 5N 12S 6S 12S 10N 1tljA 213 4.31e-33 1hv8A 367 9.08e-02 1hv8A c.37.1.19 32405 c.37.1.19 32406 1eqfA 280 2.43e-01 1eqfA a.29.2.1 16972 a.29.2.1 16973 1t7pA 698 7.24e-01 1t7pA c.55.3.5 33712 e.8.1.1 43005 1e8gA 560 8.13e-01 1qltA d.58.32.1 39455 d.145.1.1 41718 1knwA 425 9.54e-01 b.49.2.3 -4274 c.1.6.1 -5229 1b65A 375 1.00e+00 1b65A d.154.1.1 42020 1qltA 560 1.03e+00 1qltA d.58.32.1 39457 d.145.1.1 41720 1w1kA 560 1.27e+00 1kczA 413 1.36e+00 c.1.11.2 68451 d.54.1.1 68452 1ftrA 296 1.39e+00 1ftrA d.58.33.1 39485 d.58.33.1 39486 1vaoA 560 1.44e+00 1qltA d.58.32.1 39461 d.145.1.1 41724 1uouA 474 1.57e+00 a.46.2.1 -951 c.27.1.1 -6642 d.41.3.1 -9715 1k47A 337 1.70e+00 d.14.1.5 72040 d.58.26.4 72041 1f7uA 607 2.31e+00 1bs2A a.27.1.1 59673 c.26.1.1 59674 d.67.2.1 59675 1b8oA 284 2.42e+00 1b8oA c.56.2.1 33762 1p4kA 295 2.69e+00 d.153.1.5 87772 1rtm1 149 2.91e+00 1rtm1 1fdyA 297 2.97e+00 1nal3 c.1.10.1 29071 1hh1A 143 3.06e+00 1gefA c.52.1.18 61036 1pl5A 142 3.13e+00 1vc4A 254 3.21e+00 c.1.2.4 -5172 1v7oA 165 3.33e+00 unknown_sccs -10249 1ofuX 119 3.34e+00 c.37.1.22 86976 1nal1 297 3.75e+00 1nal3 9gafA 295 4.01e+00 1apyA d.153.1.5 42008 1jkfA 533 4.44e+00 c.2.1.3 71700 d.81.1.3 71701 1afb1 154 4.45e+00 1rtm1 1iyeA 309 4.48e+00 e.17.1.1 83786 1dp4A 435 4.61e+00 1dp4A c.93.1.1 35710 1fmtB 314 4.62e+00 1fmtA b.46.1.1 25759 c.65.1.1 34175 1hl2A 297 4.66e+00 c.1.10.1 83581 1ayyA 151 4.76e+00 1apyA d.153.1.5 42016 2dabA 282 4.77e+00 1daaA e.17.1.1 43274 1qqp2 218 4.87e+00 1qqp2 1f0xA 571 5.34e+00 1f0xA d.58.32.2 39483 d.145.1.1 41746 1brwA 433 5.36e+00 1brwA a.46.2.1 17764 c.27.1.1 31628 d.41.3.1 38626 1fmtA 314 5.51e+00 1fmtA b.46.1.1 25758 c.65.1.1 34174 1bs2A 607 5.87e+00 1bs2A a.27.1.1 16930 c.26.1.1 31597 d.67.2.1 39563 3pnp 289 6.03e+00 1b8oA c.56.2.1 33763 1npyA 271 6.26e+00 c.2.1.7 85995 c.58.1.5 85996 1odkA 235 6.36e+00 c.56.2.1 86863 1ufkA 254 6.58e+00 unknown_sccs -8103 2napA 723 6.69e+00 2napA b.52.2.2 26926 c.81.1.1 35334 1gudA 288 6.72e+00 c.93.1.1 83326 1r94A 118 6.99e+00 b.124.1.1 -4402 1buuA 168 7.07e+00 1rtm1 d.169.1.1 42366 h.1.1.1 45388 1p5dX 463 7.19e+00 c.84.1.1 -8554 c.84.1.1 -8555 c.84.1.1 -8556 d.129.2.1 -11029 1ipiA 123 7.37e+00 c.52.1.18 66255 1jbaA 204 7.58e+00 1rec a.39.1.5 17330 1k8cA 322 7.75e+00 c.1.7.1 72172 1i1kA 309 7.93e+00 1daaA e.17.1.1 61533 1k2yX 463 7.96e+00 c.84.1.1 68063 c.84.1.1 68064 c.84.1.1 68065 d.129.2.1 68066 1daaA 282 8.07e+00 1daaA e.17.1.1 43270 1gefA 123 8.23e+00 1gefA c.52.1.18 60465 3daaA 277 8.47e+00 1daaA e.17.1.1 43272 1nal3 297 8.60e+00 1nal3 1qysA 106 8.93e+00 unknown_sccs -13432 1g6sA 427 9.16e+00 1eps d.68.2.2 39584 1gw5M 435 9.39e+00 b.2.7.1 70631 d.110.4.2 70632 1s1pA 331 9.42e+00 c.1.7.1 -5240 1nyhA 166 9.55e+00 h.1.23.1 86403 1n7zA 334 9.87e+00 b.127.1.1 85380 1pot 325 9.95e+00 1pot c.94.1.1 35807 1mi3A 322 1.03e+01 c.1.7.1 -5257 1rkqA 282 1.05e+01 c.108.1.10 -6847 1p4cA 380 1.10e+01 c.1.4.1 -5201 1huvA 380 1.11e+01 c.1.4.1 61277 1rthA 560 1.12e+01 1rthA c.55.3.1 33576 e.8.1.2 43028 1j5yA 187 1.15e+01 a.4.5.1 71592 d.94.2.1 71593 1kwkA 645 1.16e+01 b.71.1.1 77565 c.1.8.1 77566 c.23.16.5 77567 1l1lA 739 1.18e+01 c.7.1.4 73470 1nb8A 353 1.18e+01 d.3.1.9 80385 1s98A 107 1.19e+01 1oltA 457 1.24e+01 unknown_sccs -5688 1gpjA 404 1.25e+01 a.151.1.1 65451 c.2.1.7 65452 d.58.39.1 65453 1lp3A 519 1.25e+01 b.121.5.2 74169 1p3wA 404 1.26e+01 c.67.1.3 87752 1irf 112 1.30e+01 2irfG a.4.5.23 16192 1e42A 258 1.31e+01 1e42A b.1.10.1 22316 d.105.1.1 40792 1dts 221 1.31e+01 1byi c.37.1.10 32200 1q7sA 117 1.31e+01 unknown_sccs -7522 1vhwA 253 1.34e+01 c.56.2.1 -7765 1ci8A 392 1.35e+01 e.3.1.1 64765 1a04A 215 1.35e+01 1a04A a.4.6.2 16234 c.23.1.1 31089 1c1lA 136 1.38e+01 1c1lA b.29.1.3 24219 1kp0A 402 1.39e+01 c.55.2.1 72834 d.127.1.1 72835 1nrfA 262 1.40e+01 e.3.1.1 -11780 1o9wA 177 1.50e+01 b.2.3.5 86713 1rpjA 288 1.52e+01 2dri c.93.1.1 35656 1gqyA 475 1.52e+01 c.5.1.1 83305 c.59.1.1 83306 c.72.2.1 83307 1a8q 274 1.53e+01 1brt c.69.1.12 34702 1a3gA 308 1.58e+01 1daaA e.17.1.1 43286 1kwgA 645 1.61e+01 b.71.1.1 77561 c.1.8.1 77562 c.23.16.5 77563 1scmA 60 1.64e+01 1wdcA 1zmeC 70 1.65e+01 1zmeC g.38.1.1 45081 h.1.3.1 45514 1vkeA 133 1.65e+01 1iqpA 327 1.68e+01 a.80.1.1 62649 c.37.1.20 62650 1vkbA 161 1.68e+01 1f74A 293 1.74e+01 1nal3 c.1.10.1 29079 1lc0A 294 1.74e+01 c.2.1.3 73823 d.81.1.4 73824 1gcuA 295 1.76e+01 1gcuA c.2.1.3 30063 d.81.1.4 39978 1ci9A 392 1.81e+01 e.3.1.1 64767 1dad 224 1.81e+01 1byi c.37.1.10 32204 1oo0B 110 1.86e+01 d.58.7.1 87183 1f6kA 293 1.87e+01 1nal3 c.1.10.1 29081 1lnsA 763 1.88e+01 a.40.2.1 78101 b.18.1.13 78102 c.69.1.21 78103 1ecfB 504 1.88e+01 1ecfB c.61.1.1 34054 d.153.1.1 41821 1vrtA 560 1.90e+01 1rthA c.55.3.1 33574 e.8.1.2 43023 1fjgJ 105 1.91e+01 1fjfJ d.58.15.1 39330 1r3eA 309 1.93e+01 b.122.1.1 -5118 unknown_sccs -10146 1j3mA 129 1.95e+01 1f07A 321 1.95e+01 1ezwA c.1.16.3 59560 1rkd 309 1.96e+01 1rkd c.72.1.1 34928 2ctc 307 1.96e+01 1aye c.56.5.1 33802 1c76A 136 2.05e+01 2sak d.15.5.1 37718 1ihoA 283 2.10e+01 1ihoA c.26.1.4 62390 1k2xA 177 2.12e+01 d.153.1.5 -11450 1gio 125 2.14e+01 7rsa d.5.1.1 37304 1dbs 224 2.19e+01 1byi c.37.1.10 32209 1byi 224 2.21e+01 1byi c.37.1.10 32199 1dbqA 289 2.23e+01 1qpzA c.93.1.1 35666 1kijA 390 2.23e+01 d.14.1.3 72514 d.122.1.2 72515 1dttA 560 2.34e+01 1rthA c.55.3.1 33611 e.8.1.2 43088 1bvyF 191 2.37e+01 1bvyF c.23.5.1 31207 1p8cA 145 2.39e+01 unknown_sccs -1927 1mbxC 106 2.41e+01 d.45.1.2 78929 2ctb 307 2.46e+01 1aye c.56.5.1 33803 1o0xA 262 2.50e+01 d.127.1.1 80755 1yts 278 2.51e+01 1ytw c.45.1.2 32690 1qo7A 394 2.54e+01 1qo7A c.69.1.11 34697 1rxyA 253 2.54e+01 c.56.2.1 -7834 2acr 315 2.56e+01 1frb c.1.7.1 28674 1aw7A 194 2.60e+01 1aw7A b.40.2.2 25164 d.15.6.1 37753 1j34B 123 2.61e+01 d.169.1.1 84049 1lyvA 306 2.63e+01 c.45.1.2 74348 1b3nA 412 2.64e+01 1dd8A c.95.1.1 35966 c.95.1.1 35967 1oj4A 283 2.67e+01 d.14.1.5 -9088 d.58.26.5 -10133 1dk4A 252 2.67e+01 1dk4A e.7.1.1 42970 1tsg 98 2.69e+01 1tsg 1hl6A 165 2.69e+01 d.58.7.1 83609 1j5vA 351 2.74e+01 c.72.1.1 71585 2irfG 113 2.78e+01 2irfG a.4.5.23 16185 1qwiA 143 2.81e+01 d.227.1.1 -11183 1iezA 217 2.83e+01 d.115.1.2 66129 1jflA 228 2.86e+01 c.78.2.1 71656 c.78.2.1 71657 1f20A 435 2.90e+01 b.43.4.1 64932 c.25.1.4 64933 1vpwA 340 2.93e+01 1qpzA a.35.1.5 17087 c.93.1.1 35680 1agi 125 2.94e+01 7rsa d.5.1.1 37303 1pk9A 237 2.95e+01 c.56.2.1 -7734 1qpzA 340 2.97e+01 1qpzA a.35.1.5 17097 c.93.1.1 35673 1us0A 316 2.97e+01 c.1.7.1 -5233 1dd5A 185 3.01e+01 1dd5A d.67.3.1 39564 1jcv 153 3.01e+01 1mfmA b.1.8.1 22279 1ewjA 126 3.03e+01 1ecsA d.32.1.2 59526 1eudB 396 3.11e+01 2scuB c.23.4.1 31150 d.142.1.4 41571 1rhi3 236 3.13e+01 1aym3 1kas 412 3.17e+01 1dd8A c.95.1.1 35964 c.95.1.1 35965 2dri 271 3.18e+01 2dri c.93.1.1 35637 1gox 370 3.22e+01 1gox c.1.4.1 28607 1l5jA 865 3.26e+01 a.118.15.1 73592 c.8.2.1 73593 c.83.1.1 73594 1n7kA 234 3.27e+01 c.1.10.1 85374 1ik9A 213 3.29e+01 b.59.1.1 66176 h.1.11.1 66177 1ul7A 102 3.31e+01 unknown_sccs -11020 1i8jA 323 3.31e+01 1b4kA c.1.10.3 61968 1g0hA 252 3.32e+01 1dk4A e.7.1.1 60171 1rg9A 383 3.32e+01 d.130.1.1 -11057 d.130.1.1 -11058 d.130.1.1 -11059 1dro 122 3.33e+01 1btn b.55.1.1 26954 1iu9A 111 3.34e+01 c.78.2.1 -8500 1ht9A 76 3.37e+01 4icb a.39.1.1 61252 1r3nA 462 3.39e+01 c.56.5.4 -7872 d.58.19.1 -10096 2liv 344 3.39e+01 2liv c.93.1.1 35708 1qtnA 164 3.40e+01 1pauA c.17.1.1 30999 2hmiA 558 3.45e+01 1rthA c.55.3.1 33604 e.8.1.2 43106 1wdcA 64 3.48e+01 1wdcA 1hd8A 363 3.49e+01 b.105.1.1 65803 e.3.1.1 65804 1lfpA 249 3.49e+01 e.39.1.1 73885 1dceA 567 3.51e+01 1dceA a.118.6.1 19191 b.7.4.1 23218 c.10.2.2 30867 1ecpA 238 3.52e+01 1ecpA c.56.2.1 33775 1sv6A 269 3.54e+01 1ecfA 504 3.55e+01 1ecfB c.61.1.1 34053 d.153.1.1 41820 2sak 121 3.58e+01 2sak d.15.5.1 37711 1bllE 488 3.58e+01 1lam c.56.5.3 33833 c.50.1.1 33170 1p65A 73 3.62e+01 unknown_sccs -10331 1ads 315 3.63e+01 1frb c.1.7.1 28671 1gntA 553 3.71e+01 e.26.1.1 70290 1kfiA 572 3.71e+01 c.84.1.1 68555 c.84.1.1 68556 c.84.1.1 68557 d.129.2.1 68558 1lx7A 253 3.71e+01 c.56.2.1 74329 1lucB 324 3.73e+01 1lucA c.1.16.1 29548 1vddA 228 3.76e+01 1ixxB 123 3.76e+01 1ixxB d.169.1.1 42336 1khcA 147 3.79e+01 b.34.9.2 68608 1ln4A 104 3.79e+01 d.68.4.1 74043 1ezvA 430 3.82e+01 1be3A d.185.1.1 59541 d.185.1.1 59542 1el3A 316 3.83e+01 1frb c.1.7.1 28672 1rfzA 168 3.85e+01 unknown_sccs -1206 1v5lA 103 3.87e+01 1cby 259 3.88e+01 1cby d.103.1.1 40705 1g57A 217 3.92e+01 1g57A d.115.1.2 60253 1b4eA 323 3.93e+01 1b4kA c.1.10.3 29186 1juk 248 3.95e+01 1a53 c.1.2.4 28567